coerce: as("Slinky", "SummarizedExperiment")

Description See Also Examples

Description

Create SummarizedExperiment object from Slinky object. Data will be loaded from the GCTX file, combined with metadata from the info file, and wrapped in a SummarizedExperiment object. Note that this may take a long time for the entire data set from the L1000 project. For most use cases, a subset will be desired (e.g. as(sl[1:987,1:50], SummarizedExperiment). See the loadL1K method for a more flexible way to create a SummarizedExperiment object based on various query parameters.

See Also

loadL1K

Examples

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# for build/demo only.  You MUST use your own key when using the slinky
# package.
user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
                          as='parsed')$user_key
sl <- Slinky(user_key,
                 system.file('extdata', 'demo.gctx',
                      package='slinky'),
                 system.file('extdata', 'demo_inst_info.txt',
                     package = 'slinky'))
sumex <- as(sl[, 1:20], "SummarizedExperiment")

VanAndelInstitute/slinky documentation built on Aug. 20, 2021, 1:05 p.m.